SAVANNAH — As Georgia officials and the federal government work toward deepening the river channel used by cargo ships to reach Savannah’s bustling seaport, regulatory objections that could threaten the $600 million project are being raised by a third party, neighboring South Carolina, a stakeholder that also operates the nearest competing port.

The Savannah River, which Georgia wants to deepen along 35 miles between the Port of Savannah and the Atlantic Ocean, forms a shared boundary with South Carolina. In a recent filing, South Carolina environmental regulators denied a water quality permit sought by the federal agency overseeing the project, saying it would cause unacceptable harm to the waterway’s endangered fish and fragile marshes.

The Army Corps of Engineers has appealed the rejection by South Carolina’s Department of Health and Environmental Control. If the two agencies can’t reach an agreement, the project could wind up in court.

The big question, which doesn’t have a clear answer, is how much legal weight South Carolina’s objection carries. Has Georgia’s 14-year push to deepen the river hit a mere speed bump, or has it slammed into a brick wall?

“It’s a very significant development,” said Chris DeScherer, an attorney for the Southern Environmental Law Center who has followed the Savannah project. He argues the federal Clean Water Act allows states to veto such projects.

The Army Corps says just the opposite. Col. Jeffrey Hall, the agency’s Savannah District commander, is warning South Carolina regulators that an exemption in the same law would allow the corps to ignore the state’s objections.

In an Oct. 7 letter, Hall said he’s prepared to invoke that exemption, which says states can’t stop the Army Corps from maintaining waterways for ship navigation, if South Carolina doesn’t grant the permit on appeal.